The effect of ciprofloxacin prophylaxis during haematopoietic cell transplantation on infection episodes, exposure to treatment antimicrobials and antimicrobial resistance: a single-centre retrospective cohort study

Abstract Objectives Fluroquinolone prophylaxis during haematopoietic cell transplantation (HCT) remains contentious. We aimed to determine its effectiveness and association with exposure to treatment antimicrobials and antimicrobial resistance. Methods All admission episodes for HCT (N = 400 , 372 unique patients) in a tertiary centre between January 2020 and December 2022 were studied. Allogeneic HCT (allo-HCT) recipients received prophylaxis with ciprofloxacin during chemotherapy-induced neutropenia, while autologous HCT (auto-HCT) recipients did not. Results Allo-HCT was performed for 43.3% (173/400) of patients, auto-HCT for 56.7% (227/400). Allo-HCT was associated with an average of 1.01 fewer infection episodes per 100 admission days (95% CI 0.62–1.40, P < 0.001) compared with auto-HCT. In allo-HCT, the total exposure to all antimicrobials was higher [+24.8 days of therapy (DOT)/100 admission days, P < 0.001], as was exposure to ciprofloxacin (+40.5 DOT/100 admission days, P < 0.001). By contrast, exposure to meropenem (−4.5 DOT/100 admission days, P = 0.02), piperacillin/tazobactam (−5.2 DOT/100 admission days, P < 0.001), aminoglycosides (−4.5 DOT/100 admission days, P < 0.001) and glycopeptides (−6.4 DOT/100 admission days, P < 0.001) was reduced. Enterobacteriaceae isolated during allo-HCT were more resistant to ciprofloxacin (65.5%, 19/29 versus 6.1%, 2/33, P < 0001), ceftriaxone (65.5%, 19/29 versus 9.1%, 3/33, P < 0.001), other antimicrobial classes. Vancomycin-resistant enterococci were more common in allo-HCT recipients (11%, 19/173 versus 0.9%, 2/227, P < 0.001). Inpatient mortality during allo- and auto-HCT was 9.8% (17/173) and 0.4% (1/227). respectively (P < 0.001). Conclusions Ciprofloxacin prophylaxis in allo-HCT was associated with fewer infection episodes and reduced exposure to treatment antimicrobials. Mortality in auto-HCT remained low. A significant burden of antimicrobial resistance was detected in allo-HCT recipients.


Introduction
Bacterial infections remain the leading cause of morbidity and mortality in adult patients undergoing haematopoietic cell transplantation (HCT). 1 Risk of infection is particularly high during allogeneic haematopoietic cell transplantation (allo-HCT), compared to autologous haematopoietic cell transplantation (auto-HCT), due to a plethora of factors, including prolonged chemotherapy-induced neutropenia. 2Primary antibacterial prophylaxis with fluroquinolones during the chemotherapy-induced neutropenic period has been shown to be effective in reducing mortality, as well as clinically and microbiologically documented infections. 3Despite this, there are concerns about the use of broad-spectrum agents as prophylaxis in HCT, due to rising antimicrobial resistance (AMR) rates and the risk of Clostridioides difficile infection. 4There is particular concern about fluroquinolone resistance, which rises significantly in transplant centres once prophylaxis is introduced. 5For this reason, fluroquinolone prophylaxis in HCT remains contentious. 6ne important aspect of this AMR debate is the effect of antibacterial prophylaxis on the exposure to non-fluroquinolone treatment antimicrobials.In recent Cochrane metanalysis, antimicrobial use (either prophylactic or therapeutic) was not reported as an outcome in any of the included studies. 3If fluroquinolone prophylaxis reduces infection episodes, it should also reduce the courses of other treatment antimicrobials.Within the haematology setting, these regimens usually consist of antipseudomonal penicillins, aminoglycosides, carbapenems and glycopeptides, which constitute important targets for control by antimicrobial stewardship (AMS) programmes. 7Therefore the overall effect of fluroquinolone prophylaxis on AMS is currently unclear.
In this study, we describe the infections and the burden of AMR in HCT patients in our centre during the coronavirus 2019 (COVID-19) era and assess the effectiveness of fluroquinolone prophylaxis in reducing bacterial infections.Additionally, we aim to investigate the hypothesis that primary antibacterial prophylaxis with fluroquinolones is associated with reduced patient exposure to treatment antimicrobials.

Ethics
All patients provided consent for participation in non-interventional research at the time of HCT.The study was conducted in accordance with the Ethical Principles for Medical Research Involving Human Subjects outlined in the Declaration of Helsinki and was approved by the Institutional Review Board (REC Reference Number 21/LO/0170).

Setting and study population
This study was performed in Hammersmith Hospital, a 350-bed tertiary referral hospital, part of Imperial College Healthcare NHS Trust.Hammersmith Hospital offers specialist haematology and HCT services (including matched unrelated donor, matched sibling and haploidentical HCT) in West London and is accredited by the Joint Accreditation Committee ISCT-Europe and EBMT (JACIE).All patients admitted for HCT between 1 January 2020 and 31 December 2022 were included in the study and identified through the local transplant registry.No exclusion criteria were applied.
With regards to transplant procedures, all patients were admitted to hospital in dedicated HCT wards, separated from the rest of hospital clinical areas, and nursed in HEPA filtered positive pressure ventilation isolation side rooms.They remained inpatients from the start of conditioning chemotherapy until engraftment (absolute neutrophil count higher than 0.5 × 10 9 /L, sustained >20 × 10 9 /L platelets and haemoglobin >80 g/L, free of transfusion requirements), or resolution of adverse events, whichever was later.The hospital HCT protocols mandate primary antibacterial prophylaxis with ciprofloxacin for patients receiving allo-HCT while neutropenic, whereas auto-HCT recipients do not receive any antibacterial prophylaxis.Antifungal, antiviral and anti-Pneumocystis/anti-Toxoplasma prophylaxis is also offered as per EBMT guidelines. 8In short, during the chemotherapy-induced neutropenic period, voriconazole or posaconazole is given to allo-HCT recipients as well as auto-HCT recipients with germ cell tumours, while the remaining auto-HCT recipients receive fluconazole.Aciclovir prophylaxis is given for 5 weeks from the day of HCT for allo-HCT recipients but only during the chemotherapy-induced neutropenic period for auto-HCT recipients.Co-trimoxazole anti-Pneumocystis and anti-Toxoplasma prophylaxis is given to all HCT until the day of HCT and then resumed post engraftment 5 weeks after HCT.

Management of febrile neutropenia and suspected infection
When signs and symptoms of infection develop, standard operating procedures mandate holding prophylactic antimicrobials and starting treatment with piperacillin/tazobactam and amikacin for all patients for all infectious syndromes.Teicoplanin is also started if a central venous catheter is present.For patients with penicillin allergy or patients remaining febrile after 72 hours, meropenem is substituted for piperacillintazobactam.Initial investigations include paired (aerobic and anaerobic) peripheral and central blood cultures, a throat swab for respiratory viruses and a chest X-ray.Additional cultures may be requested depending on the clinical syndrome.Antimicrobials are reviewed at 48 to 72 hours in consultation with a medical microbiologist with the aim to discontinue them early according to ECIL-4 recommendations. 6Resolution of chemotherapy-induced neutropenia is not necessary for the discontinuation of antimicrobials.All patients have rectal screens on admission for carbapenem-resistant organisms (CROs) and with nose and groin swabs for MRSA.Screening swabs are then repeated every 7 days.From March 2020, patients were also screened pre-admission with a symptom checklist and a throat swab polymerase chain reaction for SARS-CoV-2.Testing was then repeated on admission and weekly afterwards.At the end of all infection episodes, ciprofloxacin prophylaxis is resumed according to neutrophils counts.

Definitions, data sources and measurement
Comorbidities were recorded as outlined by the International Severe Acute Respiratory and Emerging Infections Consortium. 9Ethnicity was recorded as White, Asian, Black or Other as defined in the 2021 UK Census. 10eutropenia was defined as an absolute neutrophil count of ≤0.5 × 10 9 cells/L. 8Neutropenic and non-neutropenic fever were defined as previously described. 8,11CDC definitions for central line-associated bloodstream infection (CLABSI) and other tissue-focused infections were used but mucosal barrier injury-laboratory confirmed bloodstream infections (MBI-LCBIs) were recorded within neutropenic fever. 12,13n infection episode was recorded each time a patient showed signs and symptoms of infection and was started on treatment with antimicrobials.It was expressed as infection episodes per 100 admission days to allow comparison of patients with different length of stays.An invasive bacterial infection was recorded when a bacterial pathogen was isolated from a sterile site.Invasive fungal infection (IFI) was recorded when patients met criteria for probable and proven IFI as previously described. 14nfection relapse was recorded when the same pathogen was isolated during a subsequent infection episode more than 14 days and less than 60 days after the treatment for a previous episode had been completed.Polymicrobial infections refer to the growth of more than one pathogen in the same culture or in different cultures taken within 48 hours for the same infectious syndrome.Contamination was determined by the growth of a common commensal organism in a single blood culture, which was not isolated again in repeat blood cultures. 15Antimicrobial usage was calculated using days of therapy (DOTs) as previously described, and was expressed as DOTs per 100 admission days. 16ntimicrobial susceptibility results were reported using EUCAST breakpoints.All data was extracted from electronic medical records.

Statistical analysis
Statistical analysis was performed using SPSS v.29 (IBM Corp, Armonk, NY, USA).Univariable comparisons were made using the Student's t, Mann-Whitney U and Kruskal-Wallis tests for continuous variables and the Pearson's Chi-squared test for categorical variables, as appropriate.Multivariable linear regression was used to identify risk factors associated with the number of infection episodes per 100 admission days and DOTs per 100 admission days.Influential observations were detected using Baltas et al.
Cook's distance, standardized Pearson's residuals and difference in betas. 17Model parsimony was assessed using the Bayesian information criterion.Sensitivity analysis was performed for allo-HCT patients not receiving ciprofloxacin prophylaxis and 95% CIs were calculated using 10 000 bootstrap samples.The level of statistical significance was set at 0.05.No power analysis was performed.This study has been reported according to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines.

Antimicrobial exposure during HCT
With regards to antimicrobial exposure, 92.5% (160/173) of allo-HCT patients received ciprofloxacin prophylaxis during the neutropenic period, while none of the auto-HCT patients did.Ciprofloxacin prophylaxis was not administered in 13 cases due to allergy (76.9%, 10/13) or intercurrent antimicrobial treatment throughout the neutropenic period (23.1%, 3/13).Overall, in univariable analysis, allo-HCT patients had higher cumulative exposure to antimicrobials, as well as significantly higher exposure to ciprofloxacin and other antimicrobials (Table 2).On the contrary, exposure to first-and second-line treatment antimicrobials was lower.

Antimicrobial resistance results
The resistance profiles of Enterobacteriaceae, Pseudomonas aeruginosa and Enterococcus spp.are shown in Figure 2.There were Baltas et al.

Multivariable analysis results for infection episodes and exposure to treatment antimicrobials
Influential variable analysis identified one allo-HCT recipient who had a short 4-day admission and died of infection during transplantation conditioning chemotherapy.The patient was excluded from multivariable analysis.A linear regression model showed that auto-HCT was associated with 1.01 (95%CI 0.62-

Baltas et al.
in the model because none improved fitness as determined by Bayesian information criterion (Supplementary Table 3).With regards to antimicrobial exposure, linear regression results of the most parsimonious model for total antimicrobial DOT per 100 admission days are shown in Supplementary Table 4, and for individual antimicrobials in Figure 3. Model fitness estimates are presented in Supplementary Table 3.In multivariable analysis, allo-HCT was associated with significantly larger total antimicrobial exposure (24.8 DOTs per 100 admission days, 95%CI 16-33.5,P < 0.001).This was primarily driven by higher exposure to ciprofloxacin and other antimicrobials (Figure 3).On the contrary, allo-HCT patients were independently significantly less likely to be exposed to all four first-and second-line antimicrobials for the treatment of suspected infection (Figure 3).The result was preserved in sensitivity analysis excluding allo-HCT patients who did not receive ciprofloxacin prophylaxis (Supplementary Table 5).

Discussion
Our study results suggest that ciprofloxacin prophylaxis during allo-HCT was associated with reduced incidence of infection episodes and reduced exposure to first-and second-line treatment antimicrobials compared to auto-HCT patients not receiving ciprofloxacin prophylaxis.Clostridioides difficile infection was also less common in allo-HCT.Mortality in auto-HCT patients remained low.Significant AMR burden was detected in allo-HCT patients receiving ciprofloxacin prophylaxis.
Our study results indicate that ciprofloxacin prophylaxis remains effective in reducing infections, especially Gram-negative infections, in a setting of high resistance to fluroquinolones.This is important as many studies were conducted during periods when fluroquinolone resistance was particularly low. 3 Despite allo-HCT recipients being at significantly higher risk for infection compared to auto-HCT recipients, preferential use of ciprofloxacin prophylaxis in allo-HCT only was associated with reversal of this relationship in our cohort. 2Additionally, our study highlights the importance of considering the effect of antibacterial prophylaxis on the exposure to treatment antimicrobials, when assessing overall impact on AMR and AMS in future studies.9][20] Limited existing data on adult patients is also supportive. 21,22During HCT, patients are extremely vulnerable to infection, and will inevitably consume antimicrobials, for prophylaxis or for treatment. 23Therefore fluroquinolone prophylaxis might be preferable to using wider spectrum antimicrobials Other antimicrobials included all antimicrobials with fewer than five DOTs per 100 admission days.All results show the estimates of the most parsimonious model.All (antimicrobials): adjusted for age, intensive care admission, obesity, neurological disease, neutropenic fever, non-neutropenic fever, HAP or VAP, CLABSI, intrabdominal infection; MEM (Meropenem): adjusted for neutropenic fever, non-neutropenic fever, HAP or VAP, CLABSI, intrabdominal infection; TZP (piperacillin/tazobactam): adjusted for neutropenic fever, non-neutropenic fever, CLABSI.AMG (aminoglycosides): adjusted for neutropenic fever, non-neutropenic fever, HAP or VAP, CLABSI, intrabdominal infection.GLY (glycopeptides): adjusted for neutropenic fever, non-neutropenic fever, HAP or VAP, CLABSI, intrabdominal infection, neurological disease.CPFX (ciprofloxacin): adjusted for neutropenic fever, non-neutropenic fever, HAP or VAP, CLABSI, intrabdominal infection, neutropenia length.PEN (phenoxymethylpenicillin): unadjusted.Other (antimicrobials): adjusted for HAP or VAP, intrabdominal infection, intensive care admission.
Ciprofloxacin prophylaxis in stem cell transplantation for treatment.The AMS benefits from fluroquinolone prophylaxis during HCT might also be compounded by reduced rates of Clostridioides difficile infection, which has previously been described. 18,20This is thought to be secondary to fluroquinolone lack of anaerobic activity, in contrast to other antimicrobials, including beta-lactams and glycopeptides, but requires further exploration with dedicated studies. 18,20It should be noted, however, that any potential benefits from using fluroquinolones must be weighed against the rare risk of potentially long-lasting or irreversible side effects associated with these drugs. 24ur study also highlights the burden of AMR in HCT patients, particularly allo-HCT, even in a low-prevalence setting such as England.Of all isolated Enterobacteriaceae, 6.5% were resistant to meropenem, when the national average is less than 1%. 25 VRE infections were also common, and associated with high mortality in HCT recipients, indicating a significant role for this pathogen, which is frequently not covered by empirical antimicrobial regimens. 26,27igh rates of resistance to ciprofloxacin were documented, particularly in allo-HCT patients, suggesting a link with fluroquinolone prophylaxis, as resistant strains would be more likely to cause breakthrough infections.9][30] .Although our two cohorts were not directly comparable with regards to baseline risk for AMR (allo-HCT recipients are likely to have had significant higher previous exposure to antimicrobials and healthcare) and the difference in ciprofloxacin resistance rates cannot be solely attributed to the use of fluroquinolone prophylaxis, this further highlights the challenge of balancing risk and benefits for this intervention.
Strengths of our study include investigating a large recent cohort of HCT patients, especially for a single centre, and describing infections and AMR burden during the COVID-19 era.Patients were well-characterized, owing to access to an electronic medical record and there were no missing data.All eligible patients were recruited, minimizing selection bias, and there was no loss to follow up.
Limitations include the retrospective single-centre design, although this ensured all patients were treated according to the same protocols and by the same staff.We cannot exclude residual confounding when comparing antimicrobial use and infection rates in allo-HCT with auto-HCT patients, although the direction of confounding should have minimized rather than exacerbate underlying differences.A small percentage of allo-HCT patients did not receive ciprofloxacin prophylaxis, yet this did not affect results during sensitivity analysis.
In conclusion, ciprofloxacin prophylaxis during allo-HCT was associated with reduced infection episodes and reduced exposure to treatment antimicrobials compared to auto-HCT patients not receiving ciprofloxacin prophylaxis.AMR rates in allo-HCT were significantly higher.Exposure to treatment antimicrobials should be considered when weighing the risks and benefits of fluroquinolone prophylaxis in HCT.
site of infection (P < 0.001).The rate of CLABSIs was 5.3 infections per 1000 line days.

Table 2 .
Summary of infections and antimicrobials Continuous variables are presented as median (interquartile range), categorical variables as N (%).Other antimicrobials included all antimicrobials with fewer than five DOTs per 100 admission days.
Microbiologically confirmed infections refer to the number of infections with a positive culture.Polymicrobial infections refer to the growth of more than one pathogen in the same culture or in different cultures taken within 48 hours for the same infectious syndrome.
1.40, P < 0.001) additional infection episodes per 100 days of admission compared to allo-HCT.No other predictors were included Total=196 Figure 1.Causes of infection during admission for haemopoietic cell transplantation by site of infection.Strains reported were isolated